The Spaniard, who won Saturday's sprint, battled the entire race with rival Francesco Bagnaia before Marc Marquez arrived late to steal second place.
Pramac Ducati rider Martin heads the standings with 129 points, 38 ahead of Bagnaia who moved into second spot.
"There's not a lot I can say today," said Martin.
"I had a lot of doubts at the beginning of the race but finally I demonstrated to myself and all the people that need something else to prove that I was the best today.
"So, (I am) really happy. Thanks to my team because after some crashes they repaired the bike. The bike was perfect.
"Making one, one (two firsts) here in Le Mans I think was the best and perfect weekend."
Martin, a winner already this season in Portugal, did not make the best of starts from pole position, losing first place to Bagnaia on the opening lap.
The two were then locked wheel to wheel for the remainder of the race.
Bagnaia, on his factory Ducati, fought off several attacks from Martin before he finally slipped through seven laps from the end.
Bagnaia tried hard to reclaim the lead but found himself under pressure from Marquez, the six-time champion, who was eyeing victory in France following a superb ride in Spain when he came second behind Bagnaia.
Plagued by injuries and then vision issues in the past few years some feared his best days were behind him.
Marquez, however, picked up pace even as the tyres on his Gresini Ducati began to wear and picked off Bagnaia on the final lap to snatch another valuable second which lifts him to third in the standings.
